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The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants.

Colasanti J, Tremblay R, Wong AY, Coneva V, Kozaki A, Mable BK - BMC Genomics (2006)

Bottom Line: The maize INDETERMINATE1 gene, ID1, is a key regulator of the transition to flowering and the founding member of a transcription factor gene family that encodes a protein with a distinct arrangement of zinc finger motifs.The zinc fingers and surrounding sequence make up the signature ID domain (IDD), which appears to be found in all higher plant genomes.These similarities between ID1 and closely related genes in other grasses point to possible similarities in function.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada. jcolasan@uoguelph.ca

ABSTRACT

Background: The maize INDETERMINATE1 gene, ID1, is a key regulator of the transition to flowering and the founding member of a transcription factor gene family that encodes a protein with a distinct arrangement of zinc finger motifs. The zinc fingers and surrounding sequence make up the signature ID domain (IDD), which appears to be found in all higher plant genomes. The presence of zinc finger domains and previous biochemical studies showing that ID1 binds to DNA suggests that members of this gene family are involved in transcriptional regulation.

Results: Comparison of IDD genes identified in Arabidopsis and rice genomes, and all IDD genes discovered in maize EST and genomic databases, suggest that ID1 is a unique member of this gene family. High levels of sequence similarity amongst all IDD genes from maize, rice and Arabidopsis suggest that they are derived from a common ancestor. Several unique features of ID1 suggest that it is a divergent member of the maize IDD family. Although no clear ID1 ortholog was identified in the Arabidopsis genome, highly similar genes that encode proteins with identity extending beyond the ID domain were isolated from rice and sorghum. Phylogenetic comparisons show that these putative orthologs, along with maize ID1, form a group separate from other IDD genes. In contrast to ID1 mRNA, which is detected exclusively in immature leaves, several maize IDD genes showed a broad range of expression in various tissues. Further, Western analysis with an antibody that cross-reacts with ID1 protein and potential orthologs from rice and sorghum shows that all three proteins are detected in immature leaves only.

Conclusion: Comparative genomic analysis shows that the IDD zinc finger family is highly conserved among both monocots and dicots. The leaf-specific ID1 expression pattern distinguishes it from other maize IDD genes examined. A similar leaf-specific localization pattern was observed for the putative ID1 protein orthologs from rice and sorghum. These similarities between ID1 and closely related genes in other grasses point to possible similarities in function.

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Alignment of deduced ID-domain amino acid sequences of maize, rice and Arabidopsis IDD genes, as well as PCP1 from potato. Alignment of the ID domain. Green shaded areas represent amino acid identity in 70% or more of the sequences. The position of each zinc finger is by a bar and cysteine (C) and histidine (H) residues boxed; filled triangle indicate conserved C residues and open triangle indicate conserved H residues. (For the sake of simplicity, we have renamed the zinc finger order (Z1, Z2, Z3 and Z4); in a previous study (Kozaki et al., 2004) the order was Z1, Z3, Z2 and Z4.) A thick bar at the N-terminal region of the ID-domain shows the putative NLS sequence. The pink triangle represents the position intron unique to ID1 and SbID.
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Figure 2: Alignment of deduced ID-domain amino acid sequences of maize, rice and Arabidopsis IDD genes, as well as PCP1 from potato. Alignment of the ID domain. Green shaded areas represent amino acid identity in 70% or more of the sequences. The position of each zinc finger is by a bar and cysteine (C) and histidine (H) residues boxed; filled triangle indicate conserved C residues and open triangle indicate conserved H residues. (For the sake of simplicity, we have renamed the zinc finger order (Z1, Z2, Z3 and Z4); in a previous study (Kozaki et al., 2004) the order was Z1, Z3, Z2 and Z4.) A thick bar at the N-terminal region of the ID-domain shows the putative NLS sequence. The pink triangle represents the position intron unique to ID1 and SbID.

Mentions: The ID1 gene was tagged with a Ds2 transposable element that facilitated isolation of a full-length coding sequence [22]. In initial attempts to isolate the ID1 coding sequence, cDNA libraries made from 3-leaf seedling, vegetative apex, and developing inflorescence were screened with a portion of the ID1 genomic sequence. More than 50 hybridizing clones were isolated from these libraries and found to correspond to 4 different classes of cDNAs that were similar to ID1, however none of them corresponded to the maize ID1 gene. These clones were designated ID-domain genes (IDD), and given the names ZmIDDp1, ZmIDDp10, ZmIDDveg7 and ZmIDDveg9. Comparison of the ID1 cDNA sequence with the four related cDNA clones revealed that they shared a highly conserved region of ~170 amino acids (Figures 1, 2). This conserved ID-domain (IDD), has a putative nuclear localization sequence at the N-terminal border consisting of charged lysine (K) and arginine (R) residues [23], followed by four distinct zinc finger motifs. Two of the ID-domain zinc fingers have the hallmarks of the TFIIIA zinc finger class of proteins, whereas the other two zinc fingers have atypical structures and were identified by visual inspection of the deduced amino acid sequence and biochemical analysis of DNA binding properties [24].


The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants.

Colasanti J, Tremblay R, Wong AY, Coneva V, Kozaki A, Mable BK - BMC Genomics (2006)

Alignment of deduced ID-domain amino acid sequences of maize, rice and Arabidopsis IDD genes, as well as PCP1 from potato. Alignment of the ID domain. Green shaded areas represent amino acid identity in 70% or more of the sequences. The position of each zinc finger is by a bar and cysteine (C) and histidine (H) residues boxed; filled triangle indicate conserved C residues and open triangle indicate conserved H residues. (For the sake of simplicity, we have renamed the zinc finger order (Z1, Z2, Z3 and Z4); in a previous study (Kozaki et al., 2004) the order was Z1, Z3, Z2 and Z4.) A thick bar at the N-terminal region of the ID-domain shows the putative NLS sequence. The pink triangle represents the position intron unique to ID1 and SbID.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1586020&req=5

Figure 2: Alignment of deduced ID-domain amino acid sequences of maize, rice and Arabidopsis IDD genes, as well as PCP1 from potato. Alignment of the ID domain. Green shaded areas represent amino acid identity in 70% or more of the sequences. The position of each zinc finger is by a bar and cysteine (C) and histidine (H) residues boxed; filled triangle indicate conserved C residues and open triangle indicate conserved H residues. (For the sake of simplicity, we have renamed the zinc finger order (Z1, Z2, Z3 and Z4); in a previous study (Kozaki et al., 2004) the order was Z1, Z3, Z2 and Z4.) A thick bar at the N-terminal region of the ID-domain shows the putative NLS sequence. The pink triangle represents the position intron unique to ID1 and SbID.
Mentions: The ID1 gene was tagged with a Ds2 transposable element that facilitated isolation of a full-length coding sequence [22]. In initial attempts to isolate the ID1 coding sequence, cDNA libraries made from 3-leaf seedling, vegetative apex, and developing inflorescence were screened with a portion of the ID1 genomic sequence. More than 50 hybridizing clones were isolated from these libraries and found to correspond to 4 different classes of cDNAs that were similar to ID1, however none of them corresponded to the maize ID1 gene. These clones were designated ID-domain genes (IDD), and given the names ZmIDDp1, ZmIDDp10, ZmIDDveg7 and ZmIDDveg9. Comparison of the ID1 cDNA sequence with the four related cDNA clones revealed that they shared a highly conserved region of ~170 amino acids (Figures 1, 2). This conserved ID-domain (IDD), has a putative nuclear localization sequence at the N-terminal border consisting of charged lysine (K) and arginine (R) residues [23], followed by four distinct zinc finger motifs. Two of the ID-domain zinc fingers have the hallmarks of the TFIIIA zinc finger class of proteins, whereas the other two zinc fingers have atypical structures and were identified by visual inspection of the deduced amino acid sequence and biochemical analysis of DNA binding properties [24].

Bottom Line: The maize INDETERMINATE1 gene, ID1, is a key regulator of the transition to flowering and the founding member of a transcription factor gene family that encodes a protein with a distinct arrangement of zinc finger motifs.The zinc fingers and surrounding sequence make up the signature ID domain (IDD), which appears to be found in all higher plant genomes.These similarities between ID1 and closely related genes in other grasses point to possible similarities in function.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada. jcolasan@uoguelph.ca

ABSTRACT

Background: The maize INDETERMINATE1 gene, ID1, is a key regulator of the transition to flowering and the founding member of a transcription factor gene family that encodes a protein with a distinct arrangement of zinc finger motifs. The zinc fingers and surrounding sequence make up the signature ID domain (IDD), which appears to be found in all higher plant genomes. The presence of zinc finger domains and previous biochemical studies showing that ID1 binds to DNA suggests that members of this gene family are involved in transcriptional regulation.

Results: Comparison of IDD genes identified in Arabidopsis and rice genomes, and all IDD genes discovered in maize EST and genomic databases, suggest that ID1 is a unique member of this gene family. High levels of sequence similarity amongst all IDD genes from maize, rice and Arabidopsis suggest that they are derived from a common ancestor. Several unique features of ID1 suggest that it is a divergent member of the maize IDD family. Although no clear ID1 ortholog was identified in the Arabidopsis genome, highly similar genes that encode proteins with identity extending beyond the ID domain were isolated from rice and sorghum. Phylogenetic comparisons show that these putative orthologs, along with maize ID1, form a group separate from other IDD genes. In contrast to ID1 mRNA, which is detected exclusively in immature leaves, several maize IDD genes showed a broad range of expression in various tissues. Further, Western analysis with an antibody that cross-reacts with ID1 protein and potential orthologs from rice and sorghum shows that all three proteins are detected in immature leaves only.

Conclusion: Comparative genomic analysis shows that the IDD zinc finger family is highly conserved among both monocots and dicots. The leaf-specific ID1 expression pattern distinguishes it from other maize IDD genes examined. A similar leaf-specific localization pattern was observed for the putative ID1 protein orthologs from rice and sorghum. These similarities between ID1 and closely related genes in other grasses point to possible similarities in function.

Show MeSH